Showing : RPKM • reset
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.2 years ago Gordon Smyth 53k
1
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4
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5.9k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.1 years ago Sandhiya • 0
9
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10
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9.6k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.6 years ago by ▴ 20 • written 5.0 years ago by ▴ 10
1
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5
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2.0k
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bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 6.4 years ago by • 0 • written 6.4 years ago by • 0
7
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3
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4.5k
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Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 10
2
votes
1
reply
1.9k
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Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 10
1
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1
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1.5k
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
32
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16
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21k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.5 years ago by ▴ 20 • written 9.3 years ago by ▴ 200
3
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1
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1.6k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 7.7 years ago by ▴ 570 • written 7.7 years ago by ▴ 10
2
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14
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9.6k
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Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.7 years ago by ▴ 20 • written 8.2 years ago by ▴ 120
3
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2
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2.1k
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AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
9.0 years ago wcstcyx ▴ 30
4
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2
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6.0k
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How to run the rpkm function of edgeR
edger rpkm
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 20
4
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10
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6.2k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm gene length count matrix edgeR rsubread
10.0 years ago AB ▴ 110
4
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1
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2.8k
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Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 10
7
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4
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3.2k
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Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.6 years ago by 53k • written 10.6 years ago by ▴ 10
3
votes
3
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8.0k
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Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.6 years ago by ▴ 370 • written 10.6 years ago by • 0
0
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5
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3.2k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 10.7 years ago by ▴ 320 • written 10.7 years ago by ▴ 80
4
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4
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23k
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edgeR rpkm function
edger rpkm
updated 2.6 years ago by 53k • written 10.7 years ago by ▴ 30
3
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2
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17k
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how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 2.5 years ago by 53k • written 11.5 years ago by ★ 1.0k
2
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1
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1.9k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
20 results • Page 1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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